In a new (dual-boot) Ubuntu 12.10 install with encrypted home directory, brightness controls (both the slider in the Brightness and Lock settings panel and the function keys) worked out-of-the-box (hurrah!). Unfortunately, the setting was not remembered.

From thread (2), comment 13, I was able to get the system to remember the setting, but not to use it. For the record, on my system, it's necessary to adjust the path in rc.local:

#!/bin/sh -e
#
# rc.local
#
# This script is executed at the end of each multiuser runlevel.
# Make sure that the script will "exit 0" on success or any other
# value on error.
#
# In order to enable or disable this script just change the execution
# bits.
#
# By default this script does nothing.
echo 0 > /sys/class/backlight/apple_backlight/brightness
exit 0

This successfully records the brightness level of the screen at shutdown, but it has no effect on the screen brightness. I can tell the value is recorded because:

/sys/class/backlight/apple_backlight/brightness contains a value at startup

the slider in the Brightness and Lock panel is in the right position

when I change move the slider in Brightness and Lock, or when I use the brightness function keys, the screen brightness changes to the next value to the value recorded in the brightness file (for example, if I use the function keys to set the backlight to the dimmest setting where it's still on, restart and use the function keys to dim the screen once, the backlight turns off)

Does anyone have any idea how to complete the last piece of the puzzle?

This is a current bug with the Macbook Pro. How do I know? I had a Macbook Pro user start is as the bug. It has to do with the setting getting changed, but the hardware not picking up the change. For some Macbook Pro users, it doesn't matter what you change it to, or if you hard-change it manually by echoing the "setting" to the register, the flag gets changed, but the hardware does not pick up that change. It has to do with the ACPI interface to the hardware.

* There is a current work-around, although not elegant. If you get into OSX and change your brightness settings, then when you reboot and get back into Ubuntu, that last OSX brightness setting is the setting that is current when Ubuntu boots up.

I wonder if it may have something to do with whether you are booting in EFI mode. I believe that would be why Mac OS X can change the settings, when Ubuntu cannot. This article has some info on booting in EFI mode:
https://help.ubuntu.com/community/UEFI